// image to render on
private BufferedImage miniMe;
- // raw number of pixels to allocate to each column
+ /**
+ * Number of pixelsPerCol;
+ */
private float pixelsPerCol;
+ /**
+ * Number of visible columns per pixel.
+ *
+ */
+ private float colsPerPixel;
+
// raw number of pixels to allocate to each row
private float pixelsPerSeq;
private AlignmentViewPanel panel;
+ private int sequencesHeight;
+
public OverviewRenderer(AlignmentViewPanel panel, FeatureRenderer fr,
OverviewDimensions od,
AlignmentI alignment,
}
public OverviewRenderer(AlignmentViewPanel panel,
- jalview.api.FeatureRenderer fr,
- OverviewDimensions od,
+ jalview.api.FeatureRenderer fr, OverviewDimensions od,
AlignmentI alignment, ResidueShaderI resshader,
OverviewResColourFinder colFinder, boolean showProgress)
{
this.panel = panel;
finder = new FeatureColourFinder(fr);
- resColFinder = colFinder;
-
al = alignment;
shader = resshader;
+ resColFinder = colFinder;
+ this.showProgress = showProgress;
- pixelsPerCol = od.getPixelsPerCol();
- pixelsPerSeq = od.getPixelsPerSeq();
+ w = od.getWidth();
+ h = od.getHeight();
+ rows = od.getRows(alignment);
+ cols = od.getColumns(alignment);
graphHeight = od.getGraphHeight();
- miniMe = new BufferedImage(od.getWidth(), od.getHeight(),
- BufferedImage.TYPE_INT_RGB);
- this.showProgress = showProgress;
+ alignmentHeight = od.getSequencesHeight();
+
+ pixelsPerSeq = od.getPixelsPerSeq();
+ pixelsPerCol = od.getPixelsPerCol();
+ colsPerPixel = Math.max(1, 1f / pixelsPerCol);
+
}
final static int STATE_INIT = 0;
private Integer row;
- void mainLoop()
+ /**
+ * Draw alignment rows and columns onto an image. This method is asynchronous
+ * in JavaScript and interruptible in Java.
+ *
+ * Whether hidden rows or columns are drawn depends upon the type of
+ * collection.
+ *
+ * Updated to skip through high-density sequences, where columns/pixels > 1.
+ *
+ * When the process is complete, the image is passed to the AlignmentViewPanel
+ * provided by the constructor.
+ *
+ * @param rows
+ * collection of rows to be drawn
+ * @param cols
+ * collection of columns to be drawn
+ * @return image containing the drawing
+ *
+ * @author Bob Hanson 2019.07.30
+ */
+ public void drawMiniMe()
{
- while (!redraw)
+ state = STATE_INIT;
+ mainLoop();
+ }
+
+ protected void mainLoop()
+ {
+ out: while (!redraw)
{
switch (state)
{
case STATE_INIT:
- seqIndex = 0;
- pixelRow = 0;
+ init();
state = STATE_NEXT;
continue;
case STATE_NEXT:
- if (iter.hasNext())
+ if (!rowIterator.hasNext())
{
- nextRow();
+ state = STATE_DONE;
+ continue;
}
- else
+ nextRow();
+ if (!loop())
{
- state = STATE_DONE;
+ continue;
}
- break;
- case STATE_DONE:
- done();
- return;
- }
- if (delay > 0)
- {
- jsloop();
return;
+ case STATE_DONE:
+ break out;
}
+ // Java will continue without a timeout
}
done();
}
- private void jsloop()
+ private void init()
{
- if (timer == null)
- {
- timer = new Timer(delay, new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- mainLoop();
- }
+ rowIterator = rows.iterator();
+ seqIndex = 0;
+ pixelRow = 0;
+ lastRowUpdate = 0;
+ lastUpdate = 0;
+ totalPixels = w * alignmentHeight;
- });
- timer.setRepeats(false);
- timer.start();
- }
- else
+ if (showProgress)
{
- timer.restart();
+ changeSupport.firePropertyChange(UPDATE, -1, 0);
}
+
+ miniMe = new BufferedImage(w, h, BufferedImage.TYPE_INT_RGB);
+ WritableRaster raster = miniMe.getRaster();
+ DataBufferInt db = (DataBufferInt) raster.getDataBuffer();
+ Platform.timeCheck(null, Platform.TIME_MARK);
+ pixels = db.getBankData()[0];
+ bscol = cols.getOverviewBitSet();
}
private void nextRow()
{
- row = iter.next();
+ row = rowIterator.next();
// System.out.println("OR row " + r);
// get details of this alignment row
SequenceI seq = rows.getSequence(row);
// calculate where this row extends to in pixels
int endRow = Math.min(Math.round((++seqIndex) * pixelsPerSeq), h);
-
- for (int pixelCol = 0, colIndex = 0, c = bscol
- .nextSetBit(0); c >= 0; c = bscol.nextSetBit(c + 1))
+ for (int pixelCol = 0, colNext = 0, pixelEnd = 0, icol = bscol
+ .nextSetBit(0); icol >= 0; icol = getNextCol(icol, pixelEnd))
{
if (redraw)
{
break;
}
- // calculate where this column extends to in pixels
- int endCol = Math.min(Math.round((++colIndex) * pixelsPerCol), w);
-
- // don't do expensive colour determination if we're not going to use it
- // NB this is important to avoid performance issues in the overview
- // panel
+ ++colNext;
+ pixelEnd = getNextPixel(colNext, colNext);
- if (pixelCol < endCol)
+ if (pixelCol == pixelEnd)
{
- // System.out.println("OR pc ec " + pixelCol + " " + endCol);
- int rgb = getColumnColourFromSequence(allGroups, seq, c);
+ break;
+ }
+ else if (pixelCol < pixelEnd)
+ {
+ int rgb = getColumnColourFromSequence(allGroups, seq, icol);
// fill in the appropriate number of pixels
+ // System.out.println(
+ // "OR colNext=" + colNext + " " + pixelCol
+ // + "-" + pixelEnd + " icol=" + icol + " " + rgb + " "
+ // + pixelsPerCol);
for (int row = pixelRow; row < endRow; ++row)
{
- for (int col = pixelCol; col < endCol; ++col)
+ for (int col = pixelCol; col < pixelEnd; ++col)
{
// BH 2019.07.27 was:
//
ndone++;
}
}
- // }
-
- pixelCol = endCol;
+ pixelCol = pixelEnd;
// store last update value
if (showProgress)
{
- lastUpdate = sendProgressUpdate(endCol * (endRow - 1 - pixelRow),
+ lastUpdate = sendProgressUpdate(
+ pixelEnd * (endRow - 1 - pixelRow),
totalPixels, lastRowUpdate, lastUpdate);
}
}
+
}
if (pixelRow < endRow)
{
}
}
+ /**
+ * The next column is either the next set bit (when there are multiple pixels
+ * per column) or the next set bit for the column that aligns with the next
+ * pixel (when there are more columns than pixels).
+ *
+ * @param icol
+ * @param pixel
+ * @return
+ */
+ private int getNextCol(int icol, int pixel)
+ {
+ return bscol.nextSetBit(
+ pixelsPerCol >= 1 ? icol + 1 : (int) (pixel * colsPerPixel));
+ }
+
+ private int getNextPixel(int icol, int pixel)
+ {
+ return Math.min(
+ pixelsPerCol >= 1 || pixel == 0
+ ? Math.round(icol * pixelsPerCol)
+ : pixel,
+ w);
+ }
+
+ private boolean loop()
+ {
+ if (delay <= 0)
+ {
+ return false;
+ }
+ if (timer == null)
+ {
+ timer = new Timer(delay, new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ mainLoop();
+ }
+
+ });
+ timer.setRepeats(false);
+ timer.start();
+ }
+ else
+ {
+ timer.restart();
+ }
+ return true;
+ }
+
private void done()
{
Platform.timeCheck(
+ redraw,
Platform.TIME_MARK);
- overlayHiddenRegions(rows, cols);
+ overlayHiddenRegions();
if (showProgress)
{
// final update to progress bar if present
private AlignmentColsCollectionI cols;
- Iterator<Integer> iter;
+ Iterator<Integer> rowIterator;
int alignmentHeight;
int[] pixels;
- BitSet bscol = new BitSet();
+ BitSet bscol;
int w, h;
- /**
- * Draw alignment rows and columns onto an image
- *
- * @param rit
- * Iterator over rows to be drawn
- * @param cit
- * Iterator over columns to be drawn
- * @return image containing the drawing
- */
- public BufferedImage draw(AlignmentRowsCollectionI rows,
- AlignmentColsCollectionI cols)
- {
- this.rows = rows;
- this.cols = cols;
- iter = rows.iterator();
-
- w = miniMe.getWidth();
- h = miniMe.getHeight();
- alignmentHeight = h - graphHeight;
- totalPixels = w * alignmentHeight;
- lastRowUpdate = 0;
- lastUpdate = 0;
-
- if (showProgress)
- {
- changeSupport.firePropertyChange(UPDATE, -1, 0);
- }
-
- WritableRaster raster = miniMe.getRaster();
- DataBufferInt db = (DataBufferInt) raster.getDataBuffer();
- Platform.timeCheck(null, Platform.TIME_MARK);
- pixels = db.getBankData()[0];
- bscol.clear();
- for (int c : cols)
- {
- bscol.set(c);
- }
- state = STATE_INIT;
- mainLoop();
-
- return miniMe;
- }
-
/*
* Calculate progress update value and fire event
* @param rowOffset number of rows to offset calculation by
{
return (seq == null || icol >= seq.getLength()
? resColFinder.GAP_COLOUR
- : resColFinder.getResidueColour(true, shader, allGroups, seq,
- icol, finder)).getRGB();
+ : resColFinder.getResidueColourInt(true, shader, allGroups, seq,
+ icol, finder));
}
/**
* Overlay the hidden regions on the overview image
*
- * @param rows
- * collection of rows the overview is built over
- * @param cols
- * collection of columns the overview is built over
*/
- private void overlayHiddenRegions(AlignmentRowsCollectionI rows,
- AlignmentColsCollectionI cols)
+ private void overlayHiddenRegions()
{
if (cols.hasHidden() || rows.hasHidden())
{
- BufferedImage mask = buildHiddenImage(rows, cols, miniMe.getWidth(),
- miniMe.getHeight());
+ BufferedImage mask = buildHiddenImage();
Graphics2D g = (Graphics2D) miniMe.getGraphics();
g.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER,
* height of overview in pixels
* @return BufferedImage containing mask of hidden regions
*/
- private BufferedImage buildHiddenImage(AlignmentRowsCollectionI rows,
- AlignmentColsCollectionI cols, int width, int height)
+ private BufferedImage buildHiddenImage()
{
// new masking image
- BufferedImage hiddenImage = new BufferedImage(width, height,
+ BufferedImage hiddenImage = new BufferedImage(w, h,
BufferedImage.TYPE_INT_ARGB);
Color hidden = resColFinder.getHiddenColour();
Graphics2D g2d = (Graphics2D) hiddenImage.getGraphics();
+ g2d.setColor(hidden);
// set background to transparent
// g2d.setComposite(AlphaComposite.Clear);
// g2d.fillRect(0, 0, width, height);
// set next colour to opaque
g2d.setComposite(AlphaComposite.Src);
+ // System.out.println(cols.getClass().getName());
if (cols.hasHidden())
{
- int colIndex = 0;
- int pixelCol = 0;
- for (int alignmentCol : cols)
+ // AllColsCollection only
+ BitSet bs = cols.getHiddenBitSet();
+ for (int pixelCol = -1, icol2 = 0, icol = bs
+ .nextSetBit(0); icol >= 0; icol = bs.nextSetBit(icol2))
{
if (redraw)
{
break;
}
-
- // calculate where this column extends to in pixels
- int endCol = Math.min(Math.round((++colIndex) * pixelsPerCol),
- width);
-
- // endCol is one more than old endCol
- if (pixelCol < endCol)
+ icol2 = bs.nextClearBit(icol + 1);
+ int pixelEnd = getNextPixel(icol2, 0);
+ if (pixelEnd > pixelCol)
{
- // determine the colour based on the sequence and column position
- if (cols.isHidden(alignmentCol))
- {
- g2d.setColor(hidden);
- g2d.fillRect(pixelCol, 0, endCol - pixelCol, height);
- }
- pixelCol = endCol;
+ pixelCol = getNextPixel(icol, 0);
+ g2d.fillRect(pixelCol, 0, Math.max(1, pixelEnd - pixelCol),
+ h);
+ pixelCol = pixelEnd;
}
}
}
// calculate where this row extends to in pixels
int endRow = Math.min(Math.round((++seqIndex) * pixelsPerSeq),
- height);
+ h);
// get details of this alignment row
if (rows.isHidden(alignmentRow))
{
- g2d.setColor(hidden);
- g2d.fillRect(0, pixelRow, width, endRow - 1 - pixelRow);
+ g2d.fillRect(0, pixelRow, w, endRow - 1 - pixelRow);
}
pixelRow = endRow;
}
/**
* Draw the alignment annotation in the overview panel
*
- * @param g
- * the graphics object to draw on
* @param anno
* alignment annotation information
- * @param y
- * y-position for the annotation graph
- * @param cols
- * the collection of columns used in the overview panel
*/
- public void drawGraph(Graphics g, AlignmentAnnotation anno, int y,
- AlignmentColsCollectionI cols)
+ public void drawGraph(AlignmentAnnotation anno)
{
+ int y = graphHeight;
+ Graphics g = miniMe.getGraphics();
+ g.translate(0, alignmentHeight);
+
Annotation[] annotations = anno.annotations;
float max = anno.graphMax;
g.setColor(Color.white);
- int width = miniMe.getWidth();
- g.fillRect(0, 0, width, y);
+ g.fillRect(0, 0, w, y);
- int colIndex = 0;
- int pixelCol = 0;
- for (int icol : cols)
+ for (int pixelCol = 0, colNext = 0, pixelEnd = 0, len = annotations.length, icol = bscol
+ .nextSetBit(0); icol >= 0
+ && icol < len; icol = getNextCol(icol, pixelEnd))
{
if (redraw)
{
break;
}
- if (icol >= annotations.length)
- {
- break; // no more annotations to draw here
- }
- int endCol = Math.min(Math.round((++colIndex) * pixelsPerCol), width);
+ ++colNext;
+ pixelEnd = getNextPixel(colNext, colNext);
Annotation ann = annotations[icol];
if (ann != null)
{
Color color = ann.colour;
g.setColor(color == null ? Color.black : color);
-
int height = Math.min(y, (int) ((ann.value / max) * y));
- g.fillRect(pixelCol, y - height, endCol - pixelCol, height);
+ g.fillRect(pixelCol, y - height, Math.max(1, pixelEnd - pixelCol),
+ height);
}
- pixelCol = endCol;
+ pixelCol = pixelEnd;
}
+
+ g.translate(0, -alignmentHeight);
+ g.dispose();
+
if (showProgress)
{
changeSupport.firePropertyChange(UPDATE, MAX_PROGRESS - 1,
MAX_PROGRESS);
}
+
}
/**
git://source.jalview.org / jalview.git / blobdiff